Learn to use Molecular Modeling Database, or MMDB , which is Entrez's structural database brought to you by the National Institutes of Health and the National Center for Biotechnology Information. It contains an extensive collection of three-dimensional structures with detailed annotation that can be used to learn about the structure and function of many proteins. MMDB's structures were originally obtained from PBD and they contain descriptions, references and extensive multi-directional links both inside and outside of the NCBI network. There are pre-computed structural homologs, i.e. related structures or neighbors, that you can access, and extensive visualization and comparative analysis tools that you can use to examine individual structures, or multiple structures aligned.

You will learn:

  • to search MMDB using both basic and advanced query techniques
  • how to understand the detailed results you obtain
  • methods to visualize and manipulate structures using NCBIs Cn3D structural viewer
  • to locate and view structurally aligned homologs
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group Protein-centric and protein structure resources. You might find the other tutorials in the group interesting:

Pfam: Protein Domain families

UniProt: UniProt, Universal Protein Resource

RCSB PDB: RCSB Protein Data Bank

Entrez Protein: NCBI's Entrez Protein for amino acid-centric information

Structural Biology Knowledgebase: The Protein Structure Initiative Structural Biology Knowledgebase

CATEGORIES

Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.

NCBI : This category includes resources maintained at the National Center for Biotechnology Information (NCBI).

BLOG POSTS

Video Tip of the Week: BindingDB for binding affinities: Recently when I was adding videos to our SciVee collection, I noticed that there was a set of new videos about BindingDB. This database has been around for a long time, and I was surprised to realize t...

Tip of the Week: Update to NCBI's Cn3D Viewer: As I say in the tip movie, I like to visit NCBI's homepage & just roam around over there to get an idea of what's new. They develop so many bioscience tools, algorithms & other resources that there's ...

New and Updated Online Tutorials for ASTD, Entrez Protein and MMDB: Comprehensive tutorials on the ASTD, Entrez Protein, and MMDB databases enable researchers to quickly and effectively use these invaluable variation resources. Seattle, WA September 24, 2008 -- OpenHel...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Triant A Deborah et al., Most partial domains in proteins are alignment and annotation artifacts. Genome Biology (2015) doi:10.1186/s13059-015-0656-7

Gardner G Stewart et al., Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli Selected articles from The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014): Genetics The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014). BMC Genetics (2015) doi:10.1186/1471-2156-16-S2-S2

Kelley A Lawrence et al., Partial protein domains: evolutionary insights and bioinformatics challenges. Genome Biology (2015) doi:10.1186/s13059-015-0663-8

Fu Gang et al., PubChemRDF: towards the semantic annotation of PubChem compound and substance databases Graphical abstract:. Journal of Cheminformatics (2015) doi:10.1186/s13321-015-0084-4

Wong Lok Kam et al., Bioactive proteins and peptides isolated from Chinese medicines with pharmaceutical potential. Chinese Medicine (2014) doi:10.1186/1749-8546-9-19